Variant report

Variant	rs6532203
Chromosome Location	chr4:77040424-77040425
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:77040371-77040963	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:77040030..77041940-chr4:77068087..77070410,2	K562	blood:

Variant related genes	Relation type
NUP54	TF binding region
ENSG00000138750	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11723400	0.87[CEU][hapmap];0.81[TSI][hapmap]
rs11734758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11736522	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11941852	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11946345	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13108645	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13110133	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13126384	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13127201	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13135639	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13151075	0.88[YRI][hapmap]
rs14773	0.94[ASW][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]
rs4241588	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4241589	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4241590	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4288034	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4337755	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4498155	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4538520	0.87[CEU][hapmap]
rs4544733	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4552490	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4730	1.00[CEU][hapmap];0.82[CHB][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859616	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859620	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6532204	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532208	1.00[CEU][hapmap];0.95[GIH][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6829581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6838435	0.83[MKK][hapmap];0.85[YRI][hapmap]
rs6850228	0.94[ASW][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]
rs735697	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7657598	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7657823	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1009047	chr4:76989180-77077885	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv470047	chr4:77033590-77096777	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv594693	chr4:77033590-77101068	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv461558	chr4:77033725-77115553	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv594694	chr4:77033725-77115553	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	esv275315	chr4:77040424-77056493	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6532203	CXCL11	cis	multi-tissue	Pritchard
rs6532203	NUP54	cis	cerebellum	SCAN
rs6532203	ANTXR2	cis	cerebellum	SCAN
rs6532203	PHB	trans	parietal	SCAN
rs6532203	CXCL10	cis	parietal	SCAN
rs6532203	NUP54	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77028000-77068600	Weak transcription	Gastric	stomach
2	chr4:77032200-77049200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:77032600-77067600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:77033000-77044800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr4:77033000-77046800	Strong transcription	Primary B cells from peripheral blood	blood
6	chr4:77033000-77046800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:77033000-77052000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:77033200-77044400	Weak transcription	Spleen	Spleen
9	chr4:77033200-77045200	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr4:77033200-77045600	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr4:77033200-77046200	Strong transcription	Liver	Liver
12	chr4:77033200-77046600	Strong transcription	Fetal Lung	lung
13	chr4:77033200-77058200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:77033200-77066000	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr4:77033200-77068400	Weak transcription	Small Intestine	intestine
16	chr4:77033400-77040600	Weak transcription	Lung	lung
17	chr4:77033400-77041000	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr4:77033400-77041000	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr4:77033400-77041200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:77033400-77042200	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr4:77033400-77043400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:77033400-77045600	Strong transcription	Adipose Nuclei	Adipose
23	chr4:77033400-77046000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:77033400-77046000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:77033400-77046200	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr4:77033400-77046400	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr4:77033400-77046600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:77033400-77047800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr4:77033400-77048200	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr4:77033400-77052000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr4:77033400-77052200	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr4:77033400-77065600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:77033400-77066000	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr4:77033400-77066600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr4:77033600-77047600	Strong transcription	Duodenum Mucosa	Duodenum
36	chr4:77033600-77065600	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr4:77033800-77066200	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr4:77034000-77045600	Strong transcription	Fetal Intestine Large	intestine
39	chr4:77034000-77046200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr4:77034000-77054000	Strong transcription	Dnd41	blood
41	chr4:77034000-77066000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr4:77034200-77040800	Strong transcription	Osteobl	bone
43	chr4:77034200-77041600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr4:77034200-77045400	Strong transcription	Placenta	Placenta
45	chr4:77034200-77045600	Strong transcription	Fetal Thymus	thymus
46	chr4:77034200-77046600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr4:77034400-77045600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr4:77034400-77046000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr4:77034400-77067200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr4:77034600-77043200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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